Diesel engine emissions are directly influenced by the air fuel mixture within the cylinder chamber. Increasing concern over the environment impacts of the exhaust pollutants has enforced the setting of emissions legislation since the 1960s. In the last decades emissions legislations have become stricter which resulted to the introduction of multiple injection strategies and exhaust gas recirculation (EGR) in the cylinder in order to abate emissions produced. In this study, the effect of injection rate for double in-cylinder injection in combination with various EGR and bio-diesel fuel rates has been studied using CFD simulations. Taguchi orthogonal arrays have been used for reducing the number of simulations for possible combinations of different rates of injection quantities, EGR composition and bio-diesel quantities. Oneway analysis of variance technique (ANOVA) has been used to estimate the importance of the above factors to the emissions output and performance of the engine. Results showed that using statistical methods, the optimum parameters can be found for reducing the emissions output of the engine without reducing the IMEP. NOx and soot emissions for the optimized engine have been reduced by 51% and 22% respectively compared to conventional Diesel engine.